Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants

We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.     

Sputtered Nb2O5 as an effective blocking layer at conducting glass and TiO2 interfaces in ionic liquid-based dye-sensitized solar cells

The thin Nb(2)O(5) layer works as a remarkable blocking layer when deposited by the rf magnetron sputtering method between fluorine-doped tin oxide and a mesoporous TiO(2) layer, improving open-circuit photovoltage (V(oc)) and fill factor (FF) with power conversion efficiency over 5.5% at 1 sun irradiation of the dye-sensitized TiO(2) solar cells using ionic liquid electrolytes.     

MR signal change in venous thrombus relates organizing process and thrombolytic response in rabbit

Venous thrombus is subsequently organized and replaced by fibrous connective tissue. However, the sequential changes in venous thrombi are not reliably detected by current noninvasive diagnostic techniques. The purpose of this study is to reveal whether magnetic resonance (MR) can detect venous thrombus, define thrombus age and predict thrombolytic responses. Thrombus in the rabbit jugular vein was imaged with a 1.5-T MR system at 4 h and at 1, 2 and 4 weeks using three-dimensional (3D) fast asymmetric spin echo T2-weighted (T2W) and 3D-gradient echo T1-weighted (T1W) sequences. The jugular veins were histologically assessed at each time point. Magnetic resonance imaging (MRI) was also performed in vivo before and 30 min after tissue plasminogen activator (t-PA) administration. The thrombi in MRI were comparable in size to histological sections. The signal intensity (SI) of thrombi at 4 h was heterogeneously high or low on T2W or T1W images, respectively. The SI of thrombi on T2W images decreased time-dependently, but increased on T1W images at 1 and 2 weeks. Morphological analysis showed time-dependent decreases in erythrocyte, platelet and fibrin areas and time-dependent increases in smooth muscle cell, macrophage, collagen and iron areas. The t-PA administration significantly decreased thrombus volume at 4 h but not at 1, 2 and 4 weeks. Venous thrombosis can be reliably and noninvasively detected by MRI. Measurement of SI might support assessments of thrombus age and thrombolytic response.     

Comparison of Mineral Acids in Wet Digestion of Plant Materials for Flame and Flameless Atomic Absorption Measurement of Metals

Various mineral acids are compared in measuring metals in plant materials by flame and flameless atomic absorption spectrometry. NBS-SRM 1571, Orchard Leaves, is utilized as the plant material. The combination of H₂SO₄ and HNO₃ is found to be the most suitable for measuring Fe, Mn, Cu and Zn by flame atomic absorption spectroscopy, while HNO₃ is found to be the best for measuring Cu, Mn, and Pb by flameless Atomic Absorption spectroscopy.     

Spin polarization transfer during intramolecular triplet-triplet energy transfer as studied by time resolved EPR spectroscopy

Spin polarization conservation during intramolecular triplet-triplet energy transfer was studied for the phthalimide derivatives. It is shown that spin polarization transfer is useful for determining the conformation and the nature of the lowest triple (T₁) states of the donor and acceptor moieties. The polarization pattern of the acceptor triplet state was well reproduced taking into account the polarization of the donor and the mutual orientation of the donor and acceptor moieties. This technique clarified the order of the triplet sublevels in energy of the phthalimide chromophore. The T₁ states of stilbene derivatives, which have a low quantum yield of intersystem crossing under direct excitation, were also detected.     

Determination of enantiomeric purity of axially chiral biaryls

Enantiomeric purities of axially chiral biaryls with hydroxyl, amino, and carboxyl groups can be easily determined by pmr spectra using MTPA derivatives and shift reagent.     

Kinetic study of the gas-phase reaction c-C5H10 + I2 ⇄ c-C5H8 + 2HI the heat of formation of cyclopentyl radical

The kinetics of the gas-phase dehydrogenation of cyclopentane to cyclopentene is found to be consistent with a slow attack by an I atom (step 4, text) on cyclopentane in the range 282–382°C. The measured rate constants fit the Arrhenius equation, log k₄ = 11.95 ± 0.08 – (24.9 ± 0.23)/θ 1 mole^?1 sec^?1, where θ = 2.303 R T in kcal/mole. This leads to a value of ΔH = 24.3 ± 1 kcal/mole and a bond dissociation energy DH = 94.9 ± 1 kcal/mole. The latter value is identical with DH⁰(i-Pr-H) = 95 ± 1 kcal/mole and signifies that cyclopentane and the cyclopentyl radical have the same strain energy. Arrhenius parameters are deduced for all six steps in the reaction mechanism. Surface reactions are shown to be unimportant. Cyclopentyl iodide is an unstable intermediate in the reaction and the rate constant for its bimolecular formation from HI + cyclopentene is found to be log k₆ = 8.40 ± 0.29 - (26.9 ± 0.8)/θ 1 mole^?1 sec^?1. Together with the equilibrium constant, this yields for the unimolecular elimination of HI from cyclopentyl iodide, the rate constant, log k₅ = 13.3 ± 0.3 – (42.8 ± 1.2)/θ sec^?1.     

High-performance liquid chromatographic determination of methanesulphinic acid as a method for the determination of hydroxyl radicals

For the determination of hydroxyl radicals, dimethyl sulphoxide was used as a molecular probe and the methanesulphinic acid produced was determined by high-performance liquid chromatography of its Fast Yellow GC salt derivative. The results for hydroxyl radicals formed using the Fenton and hypoxanthine-xanthine oxidase systems agreed well with the theoretical values. Interferences from phenols, aromatic amines and amino acids, which give coloured substances by reaction with the diazonium salt, could be avoided. The recovery of methanesulphinic acid added to liver homogenates and incubated for 1 h at 37°C was 70.2 ± 2.1%. The detection limit for methanesulphinic acid in a sample solution was ca. 8 ng/ml.